wikipathways Schema Extraction¶
This notebook demonstrates RDF schema extraction from the wikipathways SPARQL endpoint by discovering or querying for VoID (Vocabulary of Interlinked Datasets) descriptions and some downstream uses.
Discover or get VoID Schema¶
No suitable existing VoID found, generating new VoID... Starting query: class_partitions
Finished query: class_partitions (took 0.51s) Starting query: property_partitions
Finished query: property_partitions (took 2.83s) Starting query: datatype_partitions
Finished query: datatype_partitions (took 35.99s) VoID description saved to /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_generated_void.ttl
| subject_class | subject_uri | property | property_uri | object_class | object_uri | |
|---|---|---|---|---|---|---|
| 22 | owl:Class | http://www.w3.org/2002/07/owl#Class | rdfs:subClassOf | http://www.w3.org/2000/01/rdf-schema#subClassOf | owl:Class | http://www.w3.org/2002/07/owl#Class |
| 23 | owl:ObjectProperty | http://www.w3.org/2002/07/owl#ObjectProperty | rdfs:subClassOf | http://www.w3.org/2000/01/rdf-schema#subClassOf | owl:ObjectProperty | http://www.w3.org/2002/07/owl#ObjectProperty |
| 24 | owl:Class | http://www.w3.org/2002/07/owl#Class | skos:inScheme | http://www.w3.org/2004/02/skos/core#inScheme | skos:ConceptScheme | http://www.w3.org/2004/02/skos/core#ConceptScheme |
| 25 | owl:Class | http://www.w3.org/2002/07/owl#Class | skos:inScheme | http://www.w3.org/2004/02/skos/core#inScheme | owl:Ontology | http://www.w3.org/2002/07/owl#Ontology |
| 26 | owl:DatatypeProperty | http://www.w3.org/2002/07/owl#DatatypeProperty | skos:inScheme | http://www.w3.org/2004/02/skos/core#inScheme | skos:ConceptScheme | http://www.w3.org/2004/02/skos/core#ConceptScheme |
| ... | ... | ... | ... | ... | ... | ... |
| 850 | PublicationReference | http://vocabularies.wikipathways.org/wp#Public... | foaf:page | http://xmlns.com/foaf/0.1/page | PublicationReference | http://vocabularies.wikipathways.org/wp#Public... |
| 856 | owl:Axiom | http://www.w3.org/2002/07/owl#Axiom | owl:annotatedSource | http://www.w3.org/2002/07/owl#annotatedSource | owl:ObjectProperty | http://www.w3.org/2002/07/owl#ObjectProperty |
| 857 | owl:Axiom | http://www.w3.org/2002/07/owl#Axiom | owl:annotatedSource | http://www.w3.org/2002/07/owl#annotatedSource | owl:Class | http://www.w3.org/2002/07/owl#Class |
| 866 | owl:Axiom | http://www.w3.org/2002/07/owl#Axiom | owl:annotatedProperty | http://www.w3.org/2002/07/owl#annotatedProperty | owl:AnnotationProperty | http://www.w3.org/2002/07/owl#AnnotationProperty |
| 868 | owl:Axiom | http://www.w3.org/2002/07/owl#Axiom | oboinowl:hasSynonymType | http://www.geneontology.org/formats/oboInOwl#h... | owl:AnnotationProperty | http://www.w3.org/2002/07/owl#AnnotationProperty |
833 rows × 6 columns
| subject_class | subject_uri | property | property_uri | object_class | object_uri | |
|---|---|---|---|---|---|---|
| count | 833 | 833 | 833 | 833 | 833 | 833 |
| unique | 35 | 37 | 47 | 47 | 35 | 37 |
| top | DataNode | http://vocabularies.wikipathways.org/wp#DataNode | dcterms:isPartOf | http://purl.org/dc/terms/isPartOf | DataNode | http://vocabularies.wikipathways.org/wp#DataNode |
| freq | 84 | 79 | 167 | 167 | 113 | 109 |
Class Partition Coverage Analysis¶
Query again to know how many times do we find instances of each "shape" in the dataset.
Counting instances per class...
Getting class mappings...
Calculating coverage statistics...
Coverage analysis exported to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_coverage.csv Saved to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_coverage.csv
Schema Pattern Coverage Analysis¶
For each subject class type, calculate how many entities participate in each schema pattern divided by the total number of entities of that class type. This gives coverage ratios showing what percentage of entities actually use each relationship pattern.
| subject_class | property | object_class | coverage_percent | |
|---|---|---|---|---|
| 4 | owl:DatatypeProperty | skos:inScheme | skos:ConceptScheme | 100.0 |
| 371 | DirectedInteraction | source | DataNode | 100.0 |
| 337 | TranscriptionTranslation | rdf:type | owl:Class | 100.0 |
| 336 | Stimulation | rdf:type | owl:Class | 100.0 |
| 338 | Translocation | rdf:type | owl:Class | 100.0 |
| 67 | ComplexBinding | dcterms:isPartOf | Pathway | 100.0 |
| 65 | Complex | dcterms:isPartOf | skos:Collection | 100.0 |
| 335 | Rna | rdf:type | owl:Class | 100.0 |
| 327 | DataNode | rdf:type | owl:Class | 100.0 |
| 328 | GeneProduct | rdf:type | owl:Class | 100.0 |
Average pattern coverage: 25.2% Patterns with >50% coverage: 177/833 Exported to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_pattern_coverage.csv
LinkML¶
LinkML saved to /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_linkml_schema.yaml
Mermaid diagram for LinkML Schema¶
Parsed LinkML schema: Classes = 39 Slots = 47
erDiagram
Anchor {
}
AnnotationProperty {
}
Axiom {
}
Binding {
}
Catalysis {
}
Class {
}
Collection {
}
Comment {
}
Complex {
}
ComplexBinding {
}
ConceptScheme {
}
Conversion {
}
DataNode {
}
DatatypeProperty {
}
DirectedInteraction {
}
GeneProduct {
}
GraphicalLine {
}
Group {
}
Image {
}
InfoBox {
}
Inhibition {
}
Interaction {
}
Label {
}
Metabolite {
}
ObjectProperty {
}
Ontology {
}
Pathway {
}
Person {
}
Point {
}
Protein {
}
PublicationReference {
}
PublicationXref {
}
Restriction {
}
Rna {
}
Shape {
}
State {
}
Stimulation {
}
TranscriptionTranslation {
}
Translocation {
}
Anchor ||--|o Class : "rdf_type"
Anchor ||--|o Pathway : "dcterms_isPartOf"
AnnotationProperty ||--|o AnnotationProperty : "rdfs_subPropertyOf"
Axiom ||--|o AnnotationProperty : "oboinowl_hasSynonymType"
Axiom ||--|o AnnotationProperty : "owl_annotatedProperty"
Axiom ||--|o ObjectProperty : "owl_annotatedSource"
Binding ||--|o Class : "rdf_type"
Binding ||--|o Complex : "participants"
Binding ||--|o DataNode : "source"
Binding ||--|o DataNode : "target"
Binding ||--|o Pathway : "dcterms_isPartOf"
Binding ||--|o PublicationReference : "dcterms_references"
Binding ||--|o PublicationXref : "dcterms_bibliographicCitation"
Catalysis ||--|o Class : "rdf_type"
Catalysis ||--|o Complex : "participants"
Catalysis ||--|o DataNode : "source"
Catalysis ||--|o DataNode : "target"
Catalysis ||--|o Pathway : "dcterms_isPartOf"
Catalysis ||--|o PublicationReference : "dcterms_references"
Class ||--|o AnnotationProperty : "oboinowl_inSubset"
Class ||--|o Class : "iao_0100001"
Class ||--|o Class : "owl_disjointWith"
Class ||--|o Class : "rdfs_subClassOf"
Class ||--|o ConceptScheme : "skos_inScheme"
Collection ||--|o Class : "diseaseOntologyTag"
Collection ||--|o Class : "ontologyTag"
Collection ||--|o Class : "pathwayOntologyTag"
Collection ||--|o Class : "rdf_type"
Collection ||--|o DataNode : "dc_identifier"
Collection ||--|o Image : "foaf_img"
Collection ||--|o PublicationReference : "cito_cites"
Collection ||--|o PublicationReference : "dcterms_references"
Comment ||--|o Class : "rdf_type"
Comment ||--|o Pathway : "dcterms_isPartOf"
Complex ||--|o Class : "rdf_type"
Complex ||--|o Complex : "bdbEntrezGene"
Complex ||--|o Complex : "bdbUniprot"
Complex ||--|o Complex : "participants"
Complex ||--|o DataNode : "bdbComplexPortal"
Complex ||--|o DataNode : "bdbHgncSymbol"
Complex ||--|o DataNode : "bdbReactome"
Complex ||--|o DataNode : "dc_identifier"
Complex ||--|o Pathway : "dcterms_isPartOf"
Complex ||--|o PublicationReference : "dcterms_references"
Complex ||--|o PublicationXref : "dcterms_bibliographicCitation"
Complex ||--|o Rna : "bdbEnsembl"
ComplexBinding ||--|o Class : "rdf_type"
ComplexBinding ||--|o Complex : "participants"
ComplexBinding ||--|o Pathway : "dcterms_isPartOf"
ComplexBinding ||--|o PublicationXref : "dcterms_bibliographicCitation"
Conversion ||--|o Class : "rdf_type"
Conversion ||--|o Complex : "participants"
Conversion ||--|o DataNode : "source"
Conversion ||--|o DataNode : "target"
Conversion ||--|o Pathway : "dcterms_isPartOf"
Conversion ||--|o PublicationReference : "dcterms_references"
DataNode ||--|o Class : "rdf_type"
DataNode ||--|o Comment : "hasComment"
DataNode ||--|o Complex : "bdbEntrezGene"
DataNode ||--|o Complex : "bdbUniprot"
DataNode ||--|o Complex : "participants"
DataNode ||--|o DataNode : "bdbComplexPortal"
DataNode ||--|o DataNode : "bdbHgncSymbol"
DataNode ||--|o DataNode : "bdbHmdb"
DataNode ||--|o DataNode : "bdbInChIKey"
DataNode ||--|o DataNode : "bdbKeggCompound"
DataNode ||--|o DataNode : "bdbLipidMaps"
DataNode ||--|o DataNode : "bdbReactome"
DataNode ||--|o DataNode : "dc_identifier"
DataNode ||--|o DataNode : "rdfs_seeAlso"
DataNode ||--|o Metabolite : "bdbChEBI"
DataNode ||--|o Metabolite : "bdbChemspider"
DataNode ||--|o Pathway : "dcterms_isPartOf"
DataNode ||--|o Pathway : "pav_hasVersion"
DataNode ||--|o Person : "dc_creator"
DataNode ||--|o PublicationReference : "dcterms_references"
DataNode ||--|o PublicationReference : "hasPublicationXref"
DataNode ||--|o PublicationXref : "dcterms_bibliographicCitation"
DataNode ||--|o Rna : "bdbEnsembl"
DatatypeProperty ||--|o Class : "rdfs_range"
DatatypeProperty ||--|o ConceptScheme : "skos_inScheme"
DirectedInteraction ||--|o Class : "rdf_type"
DirectedInteraction ||--|o Complex : "participants"
DirectedInteraction ||--|o DataNode : "bdbHmdb"
DirectedInteraction ||--|o DataNode : "bdbReactome"
DirectedInteraction ||--|o DataNode : "source"
DirectedInteraction ||--|o DataNode : "target"
DirectedInteraction ||--|o Metabolite : "bdbChEBI"
DirectedInteraction ||--|o Pathway : "dcterms_isPartOf"
DirectedInteraction ||--|o PublicationReference : "dcterms_references"
GeneProduct ||--|o Class : "rdf_type"
GeneProduct ||--|o Complex : "bdbEntrezGene"
GeneProduct ||--|o Complex : "bdbUniprot"
GeneProduct ||--|o DataNode : "bdbComplexPortal"
GeneProduct ||--|o DataNode : "bdbHgncSymbol"
GeneProduct ||--|o DataNode : "bdbKeggCompound"
GeneProduct ||--|o DataNode : "bdbReactome"
GeneProduct ||--|o DataNode : "dc_identifier"
GeneProduct ||--|o Metabolite : "bdbChEBI"
GeneProduct ||--|o Pathway : "dcterms_isPartOf"
GeneProduct ||--|o Pathway : "pav_hasVersion"
GeneProduct ||--|o Person : "dc_creator"
GeneProduct ||--|o PublicationReference : "dcterms_references"
GeneProduct ||--|o Rna : "bdbEnsembl"
GraphicalLine ||--|o Anchor : "hasAnchor"
GraphicalLine ||--|o Class : "rdf_type"
GraphicalLine ||--|o Comment : "hasComment"
GraphicalLine ||--|o Pathway : "dcterms_isPartOf"
GraphicalLine ||--|o Point : "hasPoint"
GraphicalLine ||--|o PublicationReference : "hasPublicationXref"
Group ||--|o Class : "rdf_type"
Group ||--|o Comment : "hasComment"
Group ||--|o PublicationReference : "hasPublicationXref"
InfoBox ||--|o Class : "rdf_type"
Inhibition ||--|o Class : "rdf_type"
Inhibition ||--|o Complex : "participants"
Inhibition ||--|o DataNode : "bdbHmdb"
Inhibition ||--|o DataNode : "source"
Inhibition ||--|o DataNode : "target"
Inhibition ||--|o Metabolite : "bdbChEBI"
Inhibition ||--|o Pathway : "dcterms_isPartOf"
Inhibition ||--|o PublicationReference : "dcterms_references"
Interaction ||--|o Anchor : "hasAnchor"
Interaction ||--|o Class : "rdf_type"
Interaction ||--|o Comment : "hasComment"
Interaction ||--|o Complex : "participants"
Interaction ||--|o DataNode : "bdbHmdb"
Interaction ||--|o DataNode : "bdbReactome"
Interaction ||--|o DataNode : "source"
Interaction ||--|o DataNode : "target"
Interaction ||--|o Metabolite : "bdbChEBI"
Interaction ||--|o Pathway : "dcterms_isPartOf"
Interaction ||--|o Point : "hasPoint"
Interaction ||--|o PublicationReference : "dcterms_references"
Interaction ||--|o PublicationReference : "hasPublicationXref"
Interaction ||--|o PublicationXref : "dcterms_bibliographicCitation"
Label ||--|o Class : "rdf_type"
Label ||--|o Comment : "hasComment"
Label ||--|o Pathway : "dcterms_isPartOf"
Label ||--|o PublicationReference : "hasPublicationXref"
Metabolite ||--|o Class : "rdf_type"
Metabolite ||--|o Complex : "bdbEntrezGene"
Metabolite ||--|o Complex : "bdbUniprot"
Metabolite ||--|o DataNode : "bdbHmdb"
Metabolite ||--|o DataNode : "bdbInChIKey"
Metabolite ||--|o DataNode : "bdbKeggCompound"
Metabolite ||--|o DataNode : "bdbLipidMaps"
Metabolite ||--|o DataNode : "bdbReactome"
Metabolite ||--|o DataNode : "dc_identifier"
Metabolite ||--|o DataNode : "rdfs_seeAlso"
Metabolite ||--|o Metabolite : "bdbChEBI"
Metabolite ||--|o Metabolite : "bdbChemspider"
Metabolite ||--|o Pathway : "dcterms_isPartOf"
Metabolite ||--|o PublicationReference : "dcterms_references"
ObjectProperty ||--|o Class : "rdfs_domain"
ObjectProperty ||--|o Class : "rdfs_range"
ObjectProperty ||--|o Class : "rdfs_subClassOf"
ObjectProperty ||--|o ConceptScheme : "skos_inScheme"
Pathway ||--|o Class : "diseaseOntologyTag"
Pathway ||--|o Class : "ontologyTag"
Pathway ||--|o Class : "pathwayOntologyTag"
Pathway ||--|o Class : "rdf_type"
Pathway ||--|o Complex : "bdbEntrezGene"
Pathway ||--|o Complex : "bdbUniprot"
Pathway ||--|o DataNode : "bdbHgncSymbol"
Pathway ||--|o DataNode : "dc_identifier"
Pathway ||--|o Image : "foaf_img"
Pathway ||--|o Pathway : "dcterms_isPartOf"
Pathway ||--|o Pathway : "pav_hasVersion"
Pathway ||--|o Person : "dc_creator"
Pathway ||--|o PublicationReference : "cito_cites"
Pathway ||--|o PublicationReference : "dcterms_references"
Pathway ||--|o Rna : "bdbEnsembl"
Point ||--|o Class : "rdf_type"
Point ||--|o Pathway : "dcterms_isPartOf"
Protein ||--|o Class : "rdf_type"
Protein ||--|o Complex : "bdbEntrezGene"
Protein ||--|o Complex : "bdbUniprot"
Protein ||--|o DataNode : "bdbHgncSymbol"
Protein ||--|o DataNode : "bdbReactome"
Protein ||--|o DataNode : "dc_identifier"
Protein ||--|o Metabolite : "bdbChEBI"
Protein ||--|o Pathway : "dcterms_isPartOf"
Protein ||--|o PublicationReference : "dcterms_references"
Protein ||--|o Rna : "bdbEnsembl"
PublicationReference ||--|o Class : "rdf_type"
PublicationReference ||--|o Pathway : "dcterms_isPartOf"
PublicationReference ||--|o PublicationReference : "cito_cites"
PublicationReference ||--|o PublicationReference : "foaf_page"
PublicationXref ||--|o Class : "rdf_type"
PublicationXref ||--|o Pathway : "dcterms_isPartOf"
Restriction ||--|o Class : "owl_someValuesFrom"
Restriction ||--|o ObjectProperty : "owl_onProperty"
Rna ||--|o Class : "rdf_type"
Rna ||--|o Complex : "bdbEntrezGene"
Rna ||--|o Complex : "bdbUniprot"
Rna ||--|o DataNode : "bdbHgncSymbol"
Rna ||--|o DataNode : "bdbKeggCompound"
Rna ||--|o DataNode : "dc_identifier"
Rna ||--|o Metabolite : "bdbChEBI"
Rna ||--|o Pathway : "dcterms_isPartOf"
Rna ||--|o PublicationReference : "dcterms_references"
Rna ||--|o Rna : "bdbEnsembl"
Shape ||--|o Class : "rdf_type"
Shape ||--|o Comment : "hasComment"
Shape ||--|o Pathway : "dcterms_isPartOf"
Shape ||--|o PublicationReference : "hasPublicationXref"
State ||--|o Class : "rdf_type"
State ||--|o Comment : "hasComment"
State ||--|o DataNode : "stateOf"
State ||--|o PublicationReference : "hasPublicationXref"
Stimulation ||--|o Class : "rdf_type"
Stimulation ||--|o Complex : "participants"
Stimulation ||--|o DataNode : "source"
Stimulation ||--|o DataNode : "target"
Stimulation ||--|o Pathway : "dcterms_isPartOf"
Stimulation ||--|o PublicationReference : "dcterms_references"
TranscriptionTranslation ||--|o Class : "rdf_type"
TranscriptionTranslation ||--|o Complex : "participants"
TranscriptionTranslation ||--|o DataNode : "source"
TranscriptionTranslation ||--|o DataNode : "target"
TranscriptionTranslation ||--|o Pathway : "dcterms_isPartOf"
TranscriptionTranslation ||--|o PublicationReference : "dcterms_references"
Translocation ||--|o Class : "rdf_type"
Translocation ||--|o Complex : "participants"
Translocation ||--|o DataNode : "source"
Translocation ||--|o DataNode : "target"
Translocation ||--|o Pathway : "dcterms_isPartOf"
LinkML pyDantic Model Generation¶
Found 37 Pydantic model classes for schema.
All 37 generated Pydantic classes: === Anchor === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] === AnnotationProperty === rdfs_subPropertyOf: typing.Optional[AnnotationProperty] === Axiom === owl_annotatedSource: typing.Optional[ObjectProperty] owl_annotatedProperty: typing.Optional[AnnotationProperty] oboinowl_hasSynonymType: typing.Optional[AnnotationProperty] === Binding === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] dcterms_bibliographicCitation: typing.Optional[PublicationXref] === Catalysis === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] === Class === rdfs_subClassOf: typing.Optional[Class] skos_inScheme: typing.Optional[ConceptScheme] oboinowl_inSubset: typing.Optional[AnnotationProperty] iao_0100001: typing.Optional[Class] owl_disjointWith: typing.Optional[Class] === Collection === rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] cito_cites: typing.Optional[PublicationReference] dc_identifier: typing.Optional[DataNode] diseaseOntologyTag: typing.Optional[Class] foaf_img: typing.Optional[Image] ontologyTag: typing.Optional[Class] pathwayOntologyTag: typing.Optional[Class] === Comment === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] === Complex === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbReactome: typing.Optional[DataNode] dc_identifier: typing.Optional[DataNode] dcterms_bibliographicCitation: typing.Optional[PublicationXref] bdbComplexPortal: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] === ComplexBinding === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_bibliographicCitation: typing.Optional[PublicationXref] === Conversion === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] === DataNode === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbChEBI: typing.Optional[Metabolite] bdbHmdb: typing.Optional[DataNode] bdbReactome: typing.Optional[DataNode] dc_identifier: typing.Optional[DataNode] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] dcterms_bibliographicCitation: typing.Optional[PublicationXref] bdbComplexPortal: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] pav_hasVersion: typing.Optional[Pathway] bdbLipidMaps: typing.Optional[DataNode] dc_creator: typing.Optional[Person] bdbKeggCompound: typing.Optional[DataNode] bdbChemspider: typing.Optional[Metabolite] rdfs_seeAlso: typing.Optional[DataNode] bdbInChIKey: typing.Optional[DataNode] === DatatypeProperty === skos_inScheme: typing.Optional[ConceptScheme] rdfs_range: typing.Optional[Class] === DirectedInteraction === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] bdbChEBI: typing.Optional[Metabolite] bdbHmdb: typing.Optional[DataNode] bdbReactome: typing.Optional[DataNode] === GeneProduct === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbChEBI: typing.Optional[Metabolite] bdbReactome: typing.Optional[DataNode] dc_identifier: typing.Optional[DataNode] bdbComplexPortal: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] pav_hasVersion: typing.Optional[Pathway] dc_creator: typing.Optional[Person] bdbKeggCompound: typing.Optional[DataNode] === GraphicalLine === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] hasPoint: typing.Optional[Point] hasAnchor: typing.Optional[Anchor] === Group === rdf_type: typing.Optional[Class] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] === InfoBox === rdf_type: typing.Optional[Class] === Inhibition === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] bdbChEBI: typing.Optional[Metabolite] bdbHmdb: typing.Optional[DataNode] === Interaction === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] bdbChEBI: typing.Optional[Metabolite] bdbHmdb: typing.Optional[DataNode] bdbReactome: typing.Optional[DataNode] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] hasPoint: typing.Optional[Point] hasAnchor: typing.Optional[Anchor] dcterms_bibliographicCitation: typing.Optional[PublicationXref] === Label === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] === LinkMLMeta === root: dict[str, typing.Any] === Metabolite === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbChEBI: typing.Optional[Metabolite] bdbHmdb: typing.Optional[DataNode] bdbReactome: typing.Optional[DataNode] dc_identifier: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbUniprot: typing.Optional[Complex] bdbLipidMaps: typing.Optional[DataNode] bdbKeggCompound: typing.Optional[DataNode] bdbChemspider: typing.Optional[Metabolite] rdfs_seeAlso: typing.Optional[DataNode] bdbInChIKey: typing.Optional[DataNode] === ObjectProperty === rdfs_subClassOf: typing.Optional[Class] skos_inScheme: typing.Optional[ConceptScheme] rdfs_range: typing.Optional[Class] rdfs_domain: typing.Optional[Class] === Pathway === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] cito_cites: typing.Optional[PublicationReference] dc_identifier: typing.Optional[DataNode] diseaseOntologyTag: typing.Optional[Class] foaf_img: typing.Optional[Image] ontologyTag: typing.Optional[Class] pathwayOntologyTag: typing.Optional[Class] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] pav_hasVersion: typing.Optional[Pathway] dc_creator: typing.Optional[Person] === Point === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] === Protein === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbChEBI: typing.Optional[Metabolite] bdbReactome: typing.Optional[DataNode] dc_identifier: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] === PublicationReference === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] cito_cites: typing.Optional[PublicationReference] foaf_page: typing.Optional[PublicationReference] === PublicationXref === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] === Restriction === owl_someValuesFrom: typing.Optional[Class] owl_onProperty: typing.Optional[ObjectProperty] === Rna === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] bdbChEBI: typing.Optional[Metabolite] dc_identifier: typing.Optional[DataNode] bdbEntrezGene: typing.Optional[Complex] bdbEnsembl: typing.Optional[Rna] bdbHgncSymbol: typing.Optional[DataNode] bdbUniprot: typing.Optional[Complex] bdbKeggCompound: typing.Optional[DataNode] === RootModel === root: ~RootModelRootType === Shape === dcterms_isPartOf: typing.Optional[Pathway] rdf_type: typing.Optional[Class] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] === State === rdf_type: typing.Optional[Class] hasPublicationXref: typing.Optional[PublicationReference] hasComment: typing.Optional[Comment] stateOf: typing.Optional[DataNode] === Stimulation === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] === TranscriptionTranslation === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] dcterms_references: typing.Optional[PublicationReference] source: typing.Optional[DataNode] target: typing.Optional[DataNode] === Translocation === dcterms_isPartOf: typing.Optional[Pathway] participants: typing.Optional[Complex] rdf_type: typing.Optional[Class] source: typing.Optional[DataNode] target: typing.Optional[DataNode]